Description Usage Arguments Details Value Examples
View source: R/graph.utility.R
Construct the labels matrix of the most specific OBO terms (as GO or HPO).
1 | specific.annotation.matrix(file = "gene2pheno.txt.gz")
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file |
text file representing the most specific associations gene-OBO. The file must be written as sequence of rows.
Each row represents a gene/protein and all its associations with an ontology term pipe separated, e.g.: gene1 |obo1|...|oboN.
The input example file used here ( |
The input plain text file representing the most specific associations gene-OBO term can be obtained by cloning the GitHub repository obogaf-parser, a perl5 module specifically designed to handle HPO and GO obo file and their gene annotation file (gaf file).
the annotation matrix of the most specific annotations (0/1): rows are genes and columns are HPO terms. Let's denote M the labels matrix. If M[i,j]=1, means that the gene i is annotated with the class j, otherwise M[i,j]=0.
1 2 | gene2pheno <- system.file("extdata/gene2pheno.txt.gz", package="HEMDAG");
spec.ann <- specific.annotation.matrix(file=gene2pheno);
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